def similar_symmetry(hkl1, hklref):
refdata = ASCII(hklref)
tstdata = ASCII(hkl1)
try:
return refdata.symm.is_similar_symmetry(tstdata.symm,
relative_length_tolerance=0.05,
absolute_angle_tolerance=1.5)
except Exception:
return False
def calc_CCset(self, hkl1, hkl2): f1 = ASCII(hkl1) f2 = ASCII(hkl2); cclst = [] for index in set(f1.data_dict).intersection(set(f2.data_dict)): I1 = f1.data_dict[index][0]; sigI1 = f1.data_dict[index][1]; I2 = f2.data_dict[index][0]; sigI2 = f2.data_dict[index][1]; cc = (I1*I2)/(sigI1*sigI2) cclst.append(cc) return cclst
def run_(self):
try:
if self.expt == 'native-sad':
self.xscale_for_sad()
self.Isa_select(6.0)
shutil.copyfile('XSCALE.LP', 'ISa_Select.LP')
shutil.copyfile('XSCALE.HKL', 'ISa_Select.HKL')
state, stats = parse_xscale_output("ISa_Select.LP")
self.scale_results['ISa_selection'] = stats
elif self.expt == 'serial-xtal':
self.xscale_for_sx()
if self.status == True:
xscale = ASCII('noSelect.HKL')
xscale.multiplicity_check()
self.scale_results['multiplicity'] = xscale.mult_list
# self.isocluster('noSelect.HKL')
self.aniso_check()
self.create_mtzs()
elif self.expt == 'inverse-beam' or self.expt == 'interleave-and-inverse-first':
pass
else:
logger.info('Error: experiment type not supported %s' %
self.expt)
self.scale_results['info'].append('Expt. type not supported')
self.scale_results['status'] = False
except Exception as e:
self.scale_results['status'] = False
logger.info('Error:{}'.format(e))
self.scale_results['info'].append(e)
return
def __init__(self, xds_ascii, **kwargs):
self.hklfile = xds_ascii
self.hkldata = ASCII(self.hklfile)
self.mtzfile = None
self.seq_file = kwargs.get('seq_file', None)
self.solvent_content = kwargs.get('solvent_content', '0.50')
self.hres = kwargs.get('hres', '1.0')
self.substr = kwargs.get('substr', "None")
self.native = kwargs.get('native', None)
self.fmt = ['CCP4_I+F', 'CCP4']
self.cell = None
self.symm = None
self.sites = kwargs.get('sites', 0)
self.atomtype = kwargs.get('atomtype', 'S')
self.nres = kwargs.get('nres', 0)
def create_mtzs(self):
lst_of_hkls = [
'noSelect.HKL', 'ISa_Select.HKL', 'Cell_Select.HKL',
'pCC_Select.HKL'
]
for hklfile in lst_of_hkls:
if os.path.isfile(hklfile):
hkl = ASCII(hklfile)
hkl.xdsconv('CCP4_I+F',
res=self.res_cut,
dirname=self.subadm,
user=self.user)
else:
logger.info('mtz-create-info:{}'.format(
'could not create mtz; file may not exist'))
pass
return
def __init__(self, ref_file, symm):
self.ref_file = ref_file
if not self.ref_file.endswith('.sca'):
self.hkl = ASCII(self.ref_file)
self.cell = self.hkl.header['!UNIT_CELL_CONSTANTS']
else:
self.cell = sub.check_output([
"cat " + self.ref_file +
" | awk 'NR>2 && NR<4 {print $1, $2, $3, $4, $5, $6}'"
],
shell=True)
self.symm = symm
self.sites = []
self.reso = []
self.ntries = [10000, 30000]
self.emins = [1.2, 1.3, 1.4, 1.5, 1.6]
self.super_sulfur = False
def xscale_for_sad(self):
self.find_HKLs()
if self.status is False:
logger.info('Error: no hkls found\n')
self.scale_results['status'] = self.status
return
try:
self.outdir_make()
os.chdir(self.subadm)
except OSError:
err = "adm folder either not there or not accessible\n"
logger.info('OSError:{}'.format(err))
self.scale_results['info'].append(err)
self.status = False
self.scale_results['status'] = self.status
if len(self.hklpaths) > 0:
if len(self.hklpaths) < 1000:
self.indexing_()
else:
logger.info('Too many hkls, so skipping the indexing check')
pass
self.create_file_links()
state, self.reference = ref_choice(self.hklpaths, fom='bfac')
if state == False and self.reference == None:
self.status = False
self.scale_results['status'] = self.status
logging.info(
'Error: bfactor-based reference choice did not work')
elif state == True and self.reference != None:
logging.info('lowest-Bfactor file: %s' % self.reference)
ref_for_cell_sg = ASCII(self.reference)
self.scale_results['space_group'] = space_group[
ref_for_cell_sg.spg][0]
self.scale_results['unit-cell'] = ref_for_cell_sg.unit_cell
self.friedel = ref_for_cell_sg.anom
self.create_inp(self.filelinks,
refs=self.reference,
reso=self.res_cut)
else:
self.create_inp(self.filelinks)
msg = "xscale-ing of native SAD data\n"
logger.info('MSG:{}'.format(msg))
try:
run_command("Scale&Merge", self.subadm, self.user,
self.xscale_cmd, 'merge.log')
except Exception:
sub.call(self.xscale_cmd, shell=True)
try:
state, stats = parse_xscale_output("XSCALE.LP")
if state is False:
self.status = False
self.scale_results['status'] = self.status
return
else:
logger.info('stat_dict:{}'.format(stats))
self.scale_results['nSAD_xscale_stats'] = stats
shutil.copyfile('XSCALE.HKL', 'nSAD.HKL')
shutil.copyfile('XSCALE.LP', 'nSAD.LP')
self.status = True
except Exception as err:
logger.info('Error: {}'.format(err))
self.scale_results['info'].append(err)
self.status = False
self.scale_results['status'] = self.status
return